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One of the nation’s largest coal producers will pay more than $27 million in fines and spend another $200 million in a settlement with the federal government. Alpha Natural Resources was fined for violating water pollution limits in Kentucky and four other Appalachian states.

The settlement is for more than 6,000 violations between 2006 and last year. Some of the violations were at mines owned by other companies—like Massey Energy—that Alpha purchased. The EPA says the company’s Appalachian mines discharged large amounts of heavy metals directly into streams.

Alpha Senior Vice President Gene Kitts said his company operates a lot of mines, and overall has a nearly perfect compliance rate.

“It’s a reflection of the people that we have out in the field at these operations, doing their best to keep the water clean, but by virtue of this consent decree, we acknowledge that we have to do better.”

Kitts said the settlement is fair, and Alpha has already implemented advanced technology to control pollution at some of its coal mines. He added that the settlement payout won’t affect ongoing operations, or cause the company to close any mines or lay off any workers.

Here’s what the EPA and U.S. Justice Department had to say in a press release:

“The unprecedented size of the civil penalty in this settlement sends a strong deterrent message to others in this industry that such egregious violations of the nation’s Clean Water Act will not be tolerated,” said Robert G. Dreher, Acting Assistant Attorney General for the Justice Department’s Environment and Natural Resources Division. “Today’s agreement is good news for communities across Appalachia, who have too often been vulnerable to polluters who disregard the law. It holds Alpha accountable and will bring increased compliance and transparency among Alpha and its many subsidiaries.”

In addition to paying the penalty, the companies must build and operate treatment systems to eliminate violations of selenium and salinity limits, and also implement comprehensive, system-wide improvements to ensure future compliance with the CWA. These improvements, which apply to all of Alpha’s operations in Appalachia, include developing and implementing an environmental management system and periodic internal and third-party environmental compliance audits.

The companies must also maintain a database to track violations and compliance efforts at each outfall, significantly improve the timeliness of responding to violations, and consult with third party experts to solve problem discharges. In the event of future violations, the companies will be required to pay stipulated penalties, which may be increased and, in some cases, doubled for continuing violations.

This is the largest penalty the EPA has ever levied under Section 402 of the Clean Water Act. After the settlement was announced, environmental groups sent out a statement criticizing the agency for letting the pollution happen in the first place.

“While it’s important that Alpha pays for its violations, EPA is still failing at its most important job; ensuring pollution like this doesn’t happen in the first place,” said Mary Anne Hitt, Director of Sierra Club’s Beyond Coal Campaign. “If we’ve learned anything from the coal chemical spill in West Virginia and the coal ash spill in North Carolina it’s that strong and pro-active up front enforcement of our clean water protections is paramount. Levying fines after the fact does nothing for the communities and waterways already harmed.”

Kentucky, West Virginia and Pennsylvania were listed as co-plaintiffs in the suit. Kentucky will receive $687,500 for the violations that happened in the commonwealth.